Thank you very much. <br><br>In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?)<br><br>Regards,<br>-Aswathy<br><br><br><div class="gmail_quote">
On Thu, Jun 17, 2010 at 7:52 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Determining how many waters is sufficient is a tough problem, try successive runs of option #3, below. As for the simpler topic of getting more hydration:<br>
<br>
1. If the issue is simply getting the channel hydrated enough to overcome some transition from dry to wet, then run a neat water box od 216 spc for 100 ps and extract a frame every 10 ps, then run genbox 10x successively using each of these frames. This should give you massive hydration.<br>
<br>
2. If that doesn't work, then you could add a new equilibration step where you posres some cap waters so that the channel can not dry out. This may allow SC's to equilibrate to a wet environment.<br>
<br>
3. If the issue is that the water is still moving out, then why not do SMD on a water into the pore and find out where the repulsion is.<br>
<br>
-- original message --<br>
<br>
Hi everyone,<br>
<br>
I have a homology model of a transporter. I want to study the ligand<br>
transport through the channel. i have done the following steps.<br>
<br>
1. Ligand has docked to the mouth of the channel<br>
2. Inserted the complex in POPC bilayer, then solvated, and equilibrated<br>
for 4ns(with position restarint on Protein & ligand)<br>
3. Then I saw tht there are very few wtaer inside the pore, Since this<br>
channel is an aqueous pore, I have added water to the channel using genbox.<br>
4. Then the complete system equilibrated for pico seconds.<br>
5,in order to select different snap shots for SMD (want to do a multiple<br>
SMDs with different starting structures.) I have run 1ns Production run and<br>
selected different frames.<br>
<br>
Suddenly I found that still there is no enough water in the pore, the water<br>
is moving away from the channel during step 4 &5?<br>
<br>
How can I solve this problem? Also how will I know how many water molecules<br>
will be sufficient for the channel?<br>
<br>
Thanks for your support.<br><font color="#888888">
<br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>